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Field-programmable gate arrays are widely considered accelerators for compute-intensive applications. A critical phase of FPGA application development is finding and mapping to the appropriate computing model. These models differ from models generally used in programming. For example, whereas parallel computing models are often based on thread execution and interaction, FPGA computing can exploit more degrees of freedom than are available in software. This enables models with highly flexible fine-grained parallelism and associative operations such as broadcast and collective response. Several case studies demonstrate the effectiveness of using FPGA-based accelerators in molecular modeling.